Rotherham had not won since 3 January but Warne struck, scoring from short range, to hand the Millers victory.
Millers keeper Mike Pollitt earlier made some excellent saves, firstly deflecting a Steve Sidwell free-kick on to his crossbar.
Pollitt later made a superb save from an Ivar Ingimarsson header and after the break the Rotherham keeper saved from Andy Hughes with his legs.
Reading boss Steve Coppell said:
"(Beating West Ham) was a flash in the pan - we proved it. A flash
in the pan with a soft underbelly.
"We had opportunities to win the game and didn't take them but I never really thought we'd give anything away.
"I think they had settled for a point because the big centre-half took the
free-kick himself and then one header later, the ball ended up in the back of the net."
Rotherham: Pollitt, Scott, Gilchrist (Hoskins 45), McIntosh, Hurst, Barker, Mullin, McLaren, Keane, Campbell-Ryce, Warne.
Subs Not Used: Montgomery, Newsham, Vernazza, Griffit.
Goals: Warne 90.
Reading: Hahnemann, Murty, Shorey, Sonko, Ingimarsson, Little, Sidwell, Newman, Hughes, Kitson, Morgan (Owusu 85).
Subs Not Used: Keown, Harper, Brooker, Young.
Ref: A Hall (W Midlands).